I got this when converting a project from 4.8 to 4.9 and I think I found the source of the problem.
At the same time, I was looking up how to properly rename projects. I noticed that using the proper ‘Create a Copy’ method for making a new, updated version of an old project places everything in a folder with the same name expect for an appended version number. However, the config and project name entries were left as they were. By renaming the old project and making sure that the folder name matches the project file name, all the warnings stopped appearing.
Similar warning issues when copying a project from 4.9.2 to 4.10 using the Launcher. Making a copy of the folder manually and using the ‘convert in place’ option eliminated warnings.
It is probably when copying the folder and then it indeed copy’s all but the engine thinks the user added files like textures and models and such are also used by the other engine version (externally used). So changing the name is only option that works or maby delete the old copy of the project also works.
Had the same problem switching form 4.11 to 4.12 (on Mac).
To solve I had to deleted the Saved folder AND rename my project file (the yourprojectname.uproject file inside the project folder)
After doing it, no more warnings at all.
Hope it helps.